Help - I need help to know what format is best for FCE

I have a lot a various videos to convert for FCE. I have generally just converted them to MOV h.264 (these are not HD) and use these in FCE.
The problem is the video and audio all has to be rendered. Also if I want to add an audio filter I can't listen to it in Real time as it has to be re-rendered.
I am growing tired of watching the progress bar creep along.
Any ideas would be appreciated.
Thanks
Rich

Sorry I should have mentioned it.
All for NSTC and the original is a recording done by GoToMeeting. It is a Windows Video Media Standard 9.
Usually I have to then play it and capture it as we don't want the full screen. I capture it with Snap Pro X, The result of that is an Apple Animation Millions IMA 4:1. with FPS of 10.
I then bring that in to FCE and put in Sequence and Render it. Can't do anything with the audio as it has to re-render it before I can hear it. After Render is has light blue lines above. After editing, it's exported as Flash FLV for the web. THe end size must be 720 pixels wide,
I have MPEG Streamclip but it has so many options, not sure what to use.
I have looked all over for something that talks about formats to use and have found nothing as they all seem to think the original Video is being imported from a camera.
Thanks for the response.
Rich

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Help - I need help to know what format is best for FCE

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